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- PDB-3hy5: Crystal structure of CRALBP -

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Basic information

Entry
Database: PDB / ID: 3hy5
TitleCrystal structure of CRALBP
ComponentsRetinaldehyde-binding protein 1
KeywordsTRANSPORT PROTEIN / lipid transfer protein / 11-cis-retinal / bothnia dystrophy / Acetylation / Cytoplasm / Disease mutation / Retinitis pigmentosa / Retinol-binding / Sensory transduction / Transport / Vision
Function / homology
Function and homology information


The retinoid cycle in cones (daylight vision) / 11-cis retinal binding / vitamin A metabolic process / response to stimulus / retinol binding / phosphatidylinositol bisphosphate binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / visual perception / cell body ...The retinoid cycle in cones (daylight vision) / 11-cis retinal binding / vitamin A metabolic process / response to stimulus / retinol binding / phosphatidylinositol bisphosphate binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / visual perception / cell body / centrosome / nucleoplasm / cytosol
Similarity search - Function
N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) ...N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RETINAL / L(+)-TARTARIC ACID / Retinaldehyde-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.04 Å
AuthorsStocker, A. / He, X. / Lobsiger, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Bothnia dystrophy is caused by domino-like rearrangements in cellular retinaldehyde-binding protein mutant R234W.
Authors: He, X. / Lobsiger, J. / Stocker, A.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinaldehyde-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8173
Polymers36,3831
Non-polymers4352
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.930, 71.930, 303.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Retinaldehyde-binding protein 1 / / Cellular retinaldehyde-binding protein


Mass: 36382.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRALBP, RLBP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12271
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 1M Sodium-potassium tartrate, 0.2M Lithium sulfate, pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97618 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97618 Å / Relative weight: 1
ReflectionResolution: 3.04→50 Å / Num. all: 9744 / Num. obs: 9692 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 89.676 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.8
Reflection shellResolution: 3.04→3.22 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1505 / Num. unique obs: 1499 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 57.68
Highest resolutionLowest resolution
Rotation2.94 Å43.44 Å
Translation2.94 Å43.44 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HX3

3hx3


Resolution: 3.04→48.13 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.272 970 10.01 %RANDOM
Rwork0.239 ---
all0.242 9690 --
obs0.242 9690 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 103.559 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 282.79 Å2 / Biso mean: 132.072 Å2 / Biso min: 46.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.689 Å20 Å20 Å2
2---0.689 Å20 Å2
3---0.765 Å2
Refinement stepCycle: LAST / Resolution: 3.04→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 31 0 2348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042398
X-RAY DIFFRACTIONf_angle_d0.7413235
X-RAY DIFFRACTIONf_chiral_restr0.046340
X-RAY DIFFRACTIONf_plane_restr0.004422
X-RAY DIFFRACTIONf_dihedral_angle_d14.391916
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.04-3.1990.3711330.3151194132799
3.199-3.40.3481350.28912131348100
3.4-3.6620.3071350.27512171352100
3.662-4.0310.2721360.26712271363100
4.031-4.6130.2571380.20812411379100
4.613-5.8110.2191410.2212711412100
5.811-48.130.2761520.2241357150997
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6272-0.2508-1.1474-0.32-2.05174.45480.4417-0.0360.25840.1147-0.1743-0.1153-1.0605-0.5373-0.22231.325-0.26610.06990.8725-0.1890.6367-4.214437.294228.0496
20.7107-1.11421.4888-1.3473.66274.86140.3144-0.18230.4246-0.95890.235-0.52912.5063-0.6133-0.3792.0784-0.76180.39910.7188-0.22080.6167-10.707630.271537.1684
30.7239-0.23880.64810.6719-1.49351.45050.7815-1.15650.75930.9141-0.38590.461-0.969-0.38270.0850.8303-0.7442-0.70170.65780.5179-0.3670.515811.149943.272
40.1353-0.0053-0.3930.2215-0.24530.13670.0644-0.33690.017-0.0906-0.13150.0532-0.17580.3265-0.00541.2389-0.4965-0.38561.07030.16680.79747.521116.151937.6235
53.22031.6869-0.35123.63372.89483.80531.0858-0.5884-0.36750.2541-0.2769-0.8373-0.3604-0.063-0.65320.9224-0.4526-0.18880.46080.05220.52784.594914.303826.4058
60.89680.45510.18470.49680.1390.6522-0.29560.2770.4093-0.68780.114-0.2274-0.79350.1120.05491.0391-0.47030.17350.4468-0.15110.44533.368423.058513.5904
71.55832.1401-0.05657.48271.9558-0.1771-0.38120.2076-0.2374-1.24220.2356-0.0938-1.3130.31660.11951.178-0.61260.0970.5457-0.11350.1989-3.956517.890713.2922
80.33490.28220.85543.48852.67951.6383-0.26250.20470.1597-0.0508-0.04280.6415-0.49990.36080.3331.246-0.534-0.17840.44320.0570.372-9.619127.43311.6774
90.1741-0.0468-0.08440.5813-1.08531.47130.04930.06110.1538-0.43750.1132-0.06890.5193-0.2703-0.00411.334-0.58650.42360.694-0.2740.745311.345131.984216.1567
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 23:41)A23 - 41
2X-RAY DIFFRACTION2(chain A and resid 42:55)A42 - 55
3X-RAY DIFFRACTION3(chain A and resid 56:85)A56 - 85
4X-RAY DIFFRACTION4(chain A and resid 86:98)A86 - 98
5X-RAY DIFFRACTION5(chain A and resid 99:143)A99 - 143
6X-RAY DIFFRACTION6(chain A and resid 144:185)A144 - 185
7X-RAY DIFFRACTION7(chain A and resid 186:255)A186 - 255
8X-RAY DIFFRACTION8(chain A and resid 256:295)A256 - 295
9X-RAY DIFFRACTION9(chain A and resid 296:306)A296 - 306

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